expose stack with z build methods from multi project object

saalfeldlab · Jul 20, 2023 · 212b38f · 212b38f
1 parent 129e6fe
commit 212b38f
Show file tree

Hide file tree

Showing 6 changed files with 19 additions and 17 deletions.
diff --git a/...-client/src/main/java/org/janelia/render/client/multisem/MFOVMontageMatchPatchClient.java b/...-client/src/main/java/org/janelia/render/client/multisem/MFOVMontageMatchPatchClient.java
@@ -102,9 +102,8 @@ public void deriveAndSaveMatchesForAllUnconnectedPairs()
 
         final MultiProjectParameters multiProject = parameters.multiProject;
         final RenderDataClient defaultDataClient = multiProject.getDataClient();
+        final List<StackWithZValues> stackWithZList = multiProject.buildListOfStackWithAllZ();
 
-        final List<StackWithZValues> stackWithZList =
-                multiProject.stackIdWithZ.buildListOfStackWithAllZ(defaultDataClient);
         for (final StackWithZValues stackWithZ : stackWithZList) {
             final StackMFOVWithZValues stackMFOVWithZValues =
                     new StackMFOVWithZValues(stackWithZ, parameters.patch.multiFieldOfViewId);

diff --git a/...a-client/src/main/java/org/janelia/render/client/multisem/UnconnectedCrossMFOVClient.java b/...a-client/src/main/java/org/janelia/render/client/multisem/UnconnectedCrossMFOVClient.java
@@ -79,8 +79,8 @@ public List<UnconnectedMFOVPairsForStack> findUnconnectedMFOVs()
             throws IOException {
 
         final RenderDataClient renderDataClient = parameters.multiProject.getDataClient();
-        final List<StackWithZValues> stackWithZList =
-                parameters.multiProject.stackIdWithZ.buildListOfStackWithAllZ(renderDataClient);
+        final List<StackWithZValues> stackWithZList = parameters.multiProject.buildListOfStackWithAllZ();
+
         final List<UnconnectedMFOVPairsForStack> unconnectedMFOVsForAllStacks = new ArrayList<>();
         for (final StackWithZValues stackWithZ : stackWithZList) {
             final UnconnectedMFOVPairsForStack unconnectedMFOVPairsForStack =

diff --git a/...java-client/src/main/java/org/janelia/render/client/parameter/MultiProjectParameters.java b/...java-client/src/main/java/org/janelia/render/client/parameter/MultiProjectParameters.java
@@ -70,16 +70,24 @@ public RenderDataClient getDataClient() {
     public MultiProjectParameters() {
     }
 
+    public String getBaseDataUrl() {
+        return baseDataUrl;
+    }
+
     public MatchCollectionId getMatchCollectionIdForStack(final StackId stackId) {
         return matchCollection == null ?
                stackId.getDefaultMatchCollectionId(deriveMatchCollectionNamesFromProject) :
                new MatchCollectionId(owner, matchCollection);
     }
 
-    public List<StackWithZValues> buildBatchedListOfStackWithZ()
+    public List<StackWithZValues> buildListOfStackWithBatchedZ()
+            throws IOException, IllegalArgumentException {
+        return stackIdWithZ.buildListOfStackWithBatchedZ(this.getDataClient());
+    }
+
+    public List<StackWithZValues> buildListOfStackWithAllZ()
             throws IOException, IllegalArgumentException {
-        final RenderDataClient renderDataClient = getDataClient();
-        return stackIdWithZ.buildListOfStackWithBatchedZ(renderDataClient);
+        return stackIdWithZ.buildListOfStackWithAllZ(this.getDataClient());
     }
 
     private synchronized void buildDataClient() {

diff --git a/...t/src/main/java/org/janelia/render/client/spark/multisem/MFOVMontageMatchPatchClient.java b/...t/src/main/java/org/janelia/render/client/spark/multisem/MFOVMontageMatchPatchClient.java
@@ -106,10 +106,8 @@ public void patchPairs(final JavaSparkContext sparkContext,
 
         final MultiProjectParameters multiProject = parameters.multiProject;
         final RenderDataClient sourceDataClient = multiProject.getDataClient();
-        final String baseDataUrl = sourceDataClient.getUrls().getBaseDataUrl();
-
-        final List<StackWithZValues> stackWithZValuesList =
-                multiProject.stackIdWithZ.buildListOfStackWithAllZ(sourceDataClient);
+        final String baseDataUrl = multiProject.getBaseDataUrl();
+        final List<StackWithZValues> stackWithZValuesList = multiProject.buildListOfStackWithAllZ();
 
         final List<StackMFOVWithZValues> stackMFOVWithZValuesList = new ArrayList<>();
         for (final StackWithZValues stackWithZValues : stackWithZValuesList) {

diff --git a/...nt/src/main/java/org/janelia/render/client/spark/multisem/UnconnectedCrossMFOVClient.java b/...nt/src/main/java/org/janelia/render/client/spark/multisem/UnconnectedCrossMFOVClient.java
@@ -104,11 +104,8 @@ public List<UnconnectedMFOVPairsForStack> findUnconnectedMFOVs(final JavaSparkCo
         LOG.info("findUnconnectedMFOVs: entry");
 
         final MultiProjectParameters multiProject = parameters.multiProject;
-        final RenderDataClient sourceDataClient = multiProject.getDataClient();
-        final String baseDataUrl = sourceDataClient.getBaseDataUrl();
-
-        final List<StackWithZValues> stackWithZValuesList =
-                multiProject.stackIdWithZ.buildListOfStackWithAllZ(sourceDataClient);
+        final String baseDataUrl = multiProject.getBaseDataUrl();
+        final List<StackWithZValues> stackWithZValuesList = multiProject.buildListOfStackWithAllZ();
 
         LOG.info("findUnconnectedMFOVs: distributing tasks for {} stacks", stackWithZValuesList.size());
 

diff --git a/...lient/src/main/java/org/janelia/render/client/spark/pipeline/AlignmentPipelineClient.java b/...lient/src/main/java/org/janelia/render/client/spark/pipeline/AlignmentPipelineClient.java
@@ -95,7 +95,7 @@ public void runWithContext(final JavaSparkContext sparkContext,
                     MultiStagePointMatchClient.Parameters.fromPipeline(alignmentPipelineParameters);
             final MultiStagePointMatchClient matchClient = new MultiStagePointMatchClient(p);
             final MultiProjectParameters multiProject = alignmentPipelineParameters.getMultiProject();
-            final List<StackWithZValues> batchedList = multiProject.buildBatchedListOfStackWithZ();
+            final List<StackWithZValues> batchedList = multiProject.buildListOfStackWithBatchedZ();
             matchClient.generatePairsAndMatchesForRunList(sparkContext,
                                                           batchedList,
                                                           alignmentPipelineParameters.getMatchRunList());